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https://github.com/pyControl

Open source software Python tool for behavioural experiment control. Part of pyControl system.

Proper citation: pyControl (RRID:SCR_021612) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/open-ephys/

Organization mission is to advance understanding of brain by promoting community ownership of neuroscience tools.Collaborative effort to develop, document, and distribute open source tools for systems neuroscience.Project aims to distribute reliable open source software as well as tools for extracellular recording and stimulation.

Proper citation: Open Ephys (RRID:SCR_021624) Copy   

•   Source: SciCrunch Registry

https://www.eneuro.org/content/12/2/ENEURO.0444-24.2025

Low-cost implant for reliable diaphragm EMG recordings in awake, behaving rats.Diaphragm EMG implant.

Proper citation: Implant for Reliable Diaphragm EMG Recordings in Awake, Behaving Rats (RRID:SCR_026968) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/ort/

Open-source apparatus to enable continuous individual monitoring, training, and testing of rats without removing them from their social environment. This system utilizes RFID technology to track individual animals, minimizing human intervention and providing precise behavioral data.

Proper citation: One-rat Turnstile (RRID:SCR_025570) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/kloostermannerflab/

Open source software tool for closed loop neuroscientific experiments capable of sub-millisecond response latency over high-rate streaming data acquired from high-count multi-electrode arrays. Used for processing and controlling closed-loop neuroscience data.

Proper citation: Falcon (RRID:SCR_023199) Copy   

•   Source: SciCrunch Registry

https://rupertoverall.net/ColonyTrack/

Software R package to process raw data from ColonyRack system. In addition to generating pre processed data and quality control information, range of high level metrics are calculated together with convenient tools for analysis.

Proper citation: ColonyTrack (RRID:SCR_023026) Copy   

•   Source: SciCrunch Registry

https://github.com/vivian-imbriotis/rpg

Software Python package written for Raspberry Pi for displaying visual stimuli and to provide real time feedback on stimulus timing. High performance python library for displaying drifting gratings on Raspberry Pi 3.

Proper citation: Raspberry Pi Grating (RRID:SCR_023157) Copy   

•   Source: SciCrunch Registry

https://github.com/KimchiLab/OpBoxPhys

Open source electrophysiology hardware and software package for simultaneous EEG and EMG acquisition from multiple subjects.

Proper citation: OpBox (RRID:SCR_023269) Copy   

•   Source: SciCrunch Registry

https://github.com/TomGeorge1234/RatInABox

Software Python toolkit for modelling locomotion and neuronal activity in continuous environments. Used to model realistic rodent locomotion and generate synthetic electrophysiological data from spatially modulated cell types.

Proper citation: RatInABox (RRID:SCR_023682) Copy   

•   Source: SciCrunch Registry

https://github.com/AdaptiveMotorControlLab/Camera_Control

Open source software package that allows video to be recorded in sync with behavior. Python GUI and scripts allows investigators to record from multiple imaging source camera feeds with associated timestamps for each frame. Python API to record video system timestamps from Imaging Source USB cameras. Package requires Windows 10, Anaconda, and Git, and is compatible with Imaging Source USB3 cameras. Part of Camera Control project.

Proper citation: Camera Control (RRID:SCR_021614) Copy   

•   Source: SciCrunch Registry

https://github.com/wildrootlab/SHARCQ

Software tools to register histological section images and cell count locations to mouse brain atlas. Semi automated workflow and GUI for automated brain slice histology alignment, registration, and cell quantification. Used to explore Allen Mouse Brain Atlas, register asymmetric slice images to atlas using manual input, and analyze region of interest data by registering locations of fluorescently labeled cells to standardized regions of Atlas.

Proper citation: SHARCQ (RRID:SCR_022498) Copy   

•   Source: SciCrunch Registry

https://github.com/jellen44/AutomaticSleepScoringTool

Software pipeline for sleep researchers to perform automatic sleep scoring for rodents. Artificial neural network for automated behavioral state classification in rats.

Proper citation: AutomaticSleepScoringTool (RRID:SCR_022300) Copy   

•   Source: SciCrunch Registry

https://github.com/haiderlab/DP-Lick-Detector

Distribution package for Dual Port Lick Detector.Package includes files relevant to building lick detector.

Proper citation: Dual Port Lick Detector (RRID:SCR_021521) Copy   

•   Source: SciCrunch Registry

https://github.com/ZuAh/Custom-fitting-of-implants

Tutorial to custom-design and -fit implants to continuous and discontinuous skull surfaces. Universal Guide for Skull Extraction and Custom-Fitting of Implants to Continuous and Discontinuous Skulls.

Proper citation: Custom-fitting-of-implants (RRID:SCR_025270) Copy   

•   Source: SciCrunch Registry

https://github.com/MaSoMoTr/MaSoMoTr

Markerless video-based tool to simultaneously track two interacting mice of the same appearance in controlled settings for quantifying behaviors such as different types of sniffing, touching, and locomotion to improve tracking accuracy under these settings without increased human effort. It incorporates conventional handcrafted tracking and deep-learning-based techniques. The tool is trained on small number of manually annotated images from basic experimental setup and outputs body masks and coordinates of the snout and tail-base for each mouse.

Proper citation: Markerless Mouse Tracking for Social Experiments (RRID:SCR_025368) Copy   

•   Source: SciCrunch Registry

https://www.dropbox.com/s/wx7aicjh4is81om/HomeCageForelimbTask.py?dl=0

Software Python tool running on Raspberry Pi computer. Used for trial timing and data logging. Part of Autonomous Training of Forelimb Motor Task system.

Proper citation: Autonomous Training of a Forelimb Motor Task (RRID:SCR_021603) Copy   

•   Source: SciCrunch Registry

https://github.com/mauriciowr/OBAT

Software tool as part of Operant Box for Auditory Tasks system.

Proper citation: Operant Box for Auditory Tasks (RRID:SCR_021604) Copy   

•   Source: SciCrunch Registry

https://github.com/mmgxw3/pipetteFindingCNN

Software application for convolutional neural network that assesses pipette positioning before patch clamp is begun to minimize patch clamping errors in electrophysiology experiments. Used for detecting pipette positioning and making patch clamping procedures.

Proper citation: Pipette Finding CNN (RRID:SCR_024992) Copy   

•   Source: SciCrunch Registry

https://github.com/PTMonteiro/GoFish_Ajuwon_etal_2022

Bonsai code for running GOFish platform for behavioural experiments in fish.

Proper citation: GoFish Ajuwon etal 2022 (RRID:SCR_022511) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/dual-port-lick-detector/

Project related to measuring licking behavior in mice.System includes device used for both real time measurement and manipulation of licking behavior in head fixed mice. System provides distribution package for Dual Port Lick Detector.Package includes files relevant to building lick detector.

Proper citation: Dual port Lick Detector project (RRID:SCR_021454) Copy   

•   Source: SciCrunch Registry